Prince Madog Cruise PD21_10 CTD Quality Report

Data Quality Report

Nutrients

End-users should be aware that SUNA nutrient data from RV Prince Madog cruises carried out subsequent to this cruise have been identified as of questionable value by Bangor University and National Oceanography Centre Liverpool staff. They became concerned that the instrument was not functioning properly and eventually ceased deploying it. While BODC have no information that the data on this cruise are problematic, they should be used with caution in light of the instrument's more recent history.

Open Data supplied by Natural Environment Research Council (NERC)

Sea-Bird Dissolved Oxygen Sensor SBE 43 and SBE 43F

The SBE 43 is a dissolved oxygen sensor designed for marine applications. It incorporates a high-performance Clark polarographic membrane with a pump that continuously plumbs water through it, preventing algal growth and the development of anoxic conditions when the sensor is taking measurements.

Two configurations are available: SBE 43 produces a voltage output and can be incorporated with any Sea-Bird CTD that accepts input from a 0-5 volt auxiliary sensor, while the SBE 43F produces a frequency output and can be integrated with an SBE 52-MP (Moored Profiler CTD) or used for OEM applications. The specifications below are common to both.

Prince Madog Cruise PD36_10 CTD Instrumentation

Instrument Descriptions

CTD Unit and Auxiliary Sensors

The CTD unit was a Sea-Bird Electronics 911 plus system (SN 09P23655-0620), with dissolved oxygen sensor. The CTD was fitted with a red (660 nm) beam transmissometer, a fluorometer, a Satlantic SUNA nitrate analyser and a LI-COR Underwater Quantum Sensor. Also attached was a Sea-Bird SBE 35 Temperature Logger to supply an independent check of temperature. All instruments were attached to a Sea-Bird SBE 32 compact carousel. The table below lists more detailed information about the various sensors.

Sampling device

Satlantic SUNA UV Nitrate Sensor

Description

The Satlantic SUNA (Submersible Ultraviolet Nitrate Analyzer) sensor is a chemical-free solution for autonomous monitoring of nitrogen-based nutrient concentrations. The sensor provides quick, continuous nitrate measurements and easily integrates into existing water monitoring systems. It provides the oppurtunity for real time nitrate calculation in a variety of environments including ocean, estuarine and freshwater systems.

SUNA incorporates the proven MBARI-ISUS nitrate measurement technology, which is in extensive use worldwide. This method of nitrate analysis is based on the absorption characteristics of dissolved inorganic compounds in the UV light spectrum. Chemicals absorb light in the UV and each has a unique absorption spectrum. The SUNA uses advanced UV absorption algorithms to compute the nitrate concentration directly, without the use of reagents. This technology has proven to be robust, sensitive and stable, operating continuously for extended periods of time in remote and harsh environments.

Sea-Bird Electronics SBE 911 and SBE 917 series CTD profilers

The SBE 911 and SBE 917 series of conductivity-temperature-depth (CTD) units are used to collect hydrographic profiles, including temperature, conductivity and pressure as standard. Each profiler consists of an underwater unit and deck unit or SEARAM. Auxiliary sensors, such as fluorometers, dissolved oxygen sensors and transmissometers, and carousel water samplers are commonly added to the underwater unit.

Underwater unit

The CTD underwater unit (SBE 9 or SBE 9 plus ) comprises a protective cage (usually with a carousel water sampler), including a main pressure housing containing power supplies, acquisition electronics, telemetry circuitry, and a suite of modular sensors. The original SBE 9 incorporated Sea-Bird's standard modular SBE 3 temperature sensor and SBE 4 conductivity sensor, and a Paroscientific Digiquartz pressure sensor. The conductivity cell was connected to a pump-fed plastic tubing circuit that could include auxiliary sensors. Each SBE 9 unit was custom built to individual specification. The SBE 9 was replaced in 1997 by an off-the-shelf version, termed the SBE 9 plus , that incorporated the SBE 3 plus (or SBE 3P) temperature sensor, SBE 4C conductivity sensor and a Paroscientific Digiquartz pressure sensor. Sensors could be connected to a pump-fed plastic tubing circuit or stand-alone.

Temperature, conductivity and pressure sensors

The conductivity, temperature, and pressure sensors supplied with Sea-Bird CTD systems have outputs in the form of variable frequencies, which are measured using high-speed parallel counters. The resulting count totals are converted to numeric representations of the original frequencies, which bear a direct relationship to temperature, conductivity or pressure. Sampling frequencies for these sensors are typically set at 24 Hz.

The temperature sensing element is a glass-coated thermistor bead, pressure-protected inside a stainless steel tube, while the conductivity sensing element is a cylindrical, flow-through, borosilicate glass cell with three internal platinum electrodes. Thermistor resistance or conductivity cell resistance, respectively, is the controlling element in an optimized Wien Bridge oscillator circuit, which produces a frequency output that can be converted to a temperature or conductivity reading. These sensors are available with depth ratings of 6800 m (aluminium housing) or 10500 m (titanium housing). The Paroscientific Digiquartz pressure sensor comprises a quartz crystal resonator that responds to pressure-induced stress, and temperature is measured for thermal compensation of the calculated pressure.

Additional sensors

Optional sensors for dissolved oxygen, pH, light transmission, fluorescence and others do not require the very high levels of resolution needed in the primary CTD channels, nor do these sensors generally offer variable frequency outputs. Accordingly, signals from the auxiliary sensors are acquired using a conventional voltage-input multiplexed A/D converter (optional). Some Sea-Bird CTDs use a strain gauge pressure sensor (Senso-Metrics) in which case their pressure output data is in the same form as that from the auxiliary sensors as described above.

Deck unit or SEARAM

Each underwater unit is connected to a power supply and data logging system: the SBE 11 (or SBE 11 plus ) deck unit allows real-time interfacing between the deck and the underwater unit via a conductive wire, while the submersible SBE 17 (or SBE 17 plus ) SEARAM plugs directly into the underwater unit and data are downloaded on recovery of the CTD. The combination of SBE 9 and SBE 17 or SBE 11 are termed SBE 917 or SBE 911, respectively, while the combinations of SBE 9 plus and SBE 17 plus or SBE 11 plus are termed SBE 917 plus or SBE 911 plus .

The Turner Designs SCUFA is a submersible fluorometer for chlorophyll and dye tracing operations that has been designed to operate in a wide range of concentrations, environmental conditions as well as operational modes (profiling or moored deployments). The instrument includes an integrated temperature probe and software which allow for automatic correction of fluorescence data from temperature effects. The superior ambient light rejection eliminates the effects of sunlight and allows the SCUFA to be used in surface waters without the need for external pumps or light shields.

Each instrument can be customised to meet user requirements. Users can choose one of the following channels: chlorophyll a, cyanobacteria (phycocyanin or phycoerythrin pigments), rhodamine WT, fluorescein and turbidity. Instrument options include turbidity, internal data logging and automatic temperature correction.

Three versions of the SCUFA are available: SCUFA I, II and III. SCUFA I and II are used for chlorophyll a applications, while SCUFA III is used for Rhodamine WT. Models II and III include a turbidity channel that is not present on model I. The SCUFA has been out of production since 2008.

Specifications

Depth rating

600 m

Detector

Photodiode

Temperature range

-2 to 40°C

Maximum sampling rate

1Hz- digital

5 Hz- analog

Resolution

12 bit- digital

1.2 mV- analog

Dynamic Range

Fluorescence

4 orders of magnitude

Turbidity

3 orders of magnitude

The table below presents the specifications for the different channels.

LI-COR LI-192 Underwater Quantum Sensor

The LI-192 Underwater Quantum Sensor is used to measure photosynthetic photon flux density and is cosine corrected. The sensor is often referred to as LI-192SA or LI-192SB (the LI-192SB model was superseded by LI-192SA). One of the main differences is that the LI-192SA model includes a built-in voltage output for interfacing with NexSens iSIC and SDL data loggers.

Sensor specifications, current at January 2012, are given in the table below. More information can be found in the manufacturer's LI-192SA and LI-192SB specification sheets.

SeaTech Transmissometer

Introduction

The transmissometer is designed to accurately measure the the amount of light transmitted by a modulated Light Emitting Diode (LED) through a fixed-length in-situ water column to a synchronous detector.

Specifications

Water path length: 5 cm (for use in turbid waters) to 1 m (for use in clear ocean waters).

Notes

The instrument can be interfaced to Aanderaa RCM7 current meters. This is achieved by fitting the transmissometer in a slot cut into a customized RCM4-type vane.

A red LED (660 nm) is used for general applications looking at water column sediment load. However, green or blue LEDs can be fitted for specilised optics applications. The light source used is identified by the BODC parameter code.

Prince Madog Cruise PD36_10 CTD Processing

Originator's Data Processing

Sampling Strategy

A total of 39 CTD profiles were performed during the cruise throughout Liverpool Bay. However, good data were only logged during 38 profiles. Cast028 was abandoned as the ship was drifting over the top of a mooring and the CTD was hauled in quickly to allow the ship to manoeuvre. Data were measured at 24 Hz and logged to a PC running SEASAVE, Sea-Bird's data acquisition software. Rosette bottles were fired throughout the water column on the upcast of the CTD profiles. Independent temperature data were recorded at the time of each bottle firing.

Salinity samples were taken from near-bed bottles, then returned to Bangor University (BU), where salinity was determined using a Portasal salinometer that was calibrated to standard seawater. The raw Sea-Bird data, configuration and bottle files were supplied to BODC for further processing.

BODC Processing

Data Processing

The raw CTD files were processed through the Sea-Bird SBE Data Processing software version 7.20e. Binary (.HEX) files were converted to engineering units and ASCII format (.CNV) using the DATCNV program.

Sea-Bird bottle files (.BTL), with information on pressure and other logged readings at the time of bottle firing, were also generated during the data conversion process.

WILDEDIT was not run on the data as no pressure spikes were present in the casts. FILTER was run on the pressure channel using the recommended time filter of 0.15 s.

Sea-Bird software program ALIGN CTD was run to advance conductivity by 0 s and oxygen by 3 s (within the typical range given in the Sea-Bird manual). No adjustment was made to the temperature channel as the fast sensor response time renders this unnecessary, according to the Sea-Bird literature.

To compensate for conductivity cell thermal mass effects, the data files were run through CELLTM, using alpha = 0.03, 1/beta = 7, typical values for this CTD model given in the Sea-Bird literature. LOOP EDIT was run to identify scans which were affected by ship heave. Salinity, density (Sigma-theta kg m -3 ) and oxygen concentration (ml l -1 ) were then calculated and added to the output files using the DERIVE program. BINAVERAGE was used to bin the data (both upcasts and downcasts) to 10 Hz and remove cycles flagged by LOOP EDIT. Finally, the first oxygen concentration channel and first salinity channel (both generated by DATCNV using data un-adjusted by ALIGN CTD and CELLTM) were dropped using STRIP.

Reformatting

The data were converted from ASCII format into BODC internal format using a BODC transfer function. The following table shows how the variables within the ASCII files were mapped to appropriate BODC parameter codes:

Originator's Parameter Name

Units

Description

BODC Parameter Code

Units

Comments

Pressure, Digiquartz

dbar

Pressure of water body on profiling pressure sensor

PRESPR01

dbar

-

Conductivity

S m -1

Electrical conductivity of the water column by CTD

CNDCST01

S m -1

-

Oxygen raw, SBE 43

Volts

Instrument output (voltage) from SBE 43 sensor

OXYVTLN1

Volts

Intermediate voltage channel not included in the final dataset.

Oxygen, SBE 43

ml l -1

Dissolved oxygen concentration from SBE 43 sensor

DOXYSU01

µmol l -1

Converted from ml l -1 to µmol l -1 by multiplying the original value by 44.66.

Salinity, Practical

-

Practical salinity of the water body by CTD

PSALCU01

-

Generated by Sea-Bird software from CTD temperature and conductivity data. Uncalibrated channel not included in the final dataset.

Generated by BODC during transfer using the Benson and Krause (1984) algorithm.

Screening

Reformatted CTD data were visualised using the in-house graphical editor EDSERPLO. Downcasts and upcasts were differentiated and the limits manually flagged. No data values were edited or deleted. Quality control flags were applied to data as necessary.

Banking

Once quality control screening was complete, CTD downcasts for all casts (except cast028) were loaded into BODC's shelf sea database under the Oracle Relational Database Management System. Cast028 was not loaded as the CTD cast was terminated early when the RV Prince Madog drifted over a CEFAS Smartbuoy.

These data have since (2013) been extracted from the relational database and transferred into BODC internal format for distribution as series (complete profiles).

References

Benson, BB and Krause, D (1984). The concentration and isotopic fractionation of oxygen dissolved in freshwater and seawater in equilibrium with the atmosphere. Limnol. Oceanogr., 29(3), 620-632

UNESCO, 1981. Background papers and supporting data on the International Equation of State of Seawater 1980. UNESCO Technical Papers in Marine Science No. 38, 192pp

Field Calibrations

Salinity

36 distinct salinity values (obtained from water samples from the CTD rosette) were compared to CTD salinity. 1 datum point was identified as an outlier (cast002) and removed from the analysis. The mean offset between CTD salinity and independent salinity (Autosal salinity - CTD salinity) for this dataset was found, using linear regression, to be significantly related to independent salinity at a 95% confidence level. However, this relationship was not used as the regression residuals were not normally distributed. This compromised the statistical validity of the regression. Therefore, a calibration equation was derived from the mean offset, based on 35 observations, such that: calibrated salinity = measured CTD salinity - 0.013449. The RMS error for this dataset is 0.003577 and the standard deviation = 0.003629.

Temperature

184 independent temperature values were compared to CTD temperature. 19 data points were excluded from the analysis because they were sampled on temperature gradients. The temperature offset (SBE 35 temperature - CTD temperature) was found, using regression analysis, not to be statistically related to SBE 35 temperature at a 95% confidence level. The mean offset =-0.000904 °C and the standard deviation for this dataset = 0.002489 °C. This is at the lowest level of accuracy for both the SBE 35 and Sea-Bird 911 plus CTD (+/- 0.001 °C). Therefore, there was no adjustment to the CTD temperature resulting from the application of manufacturers coefficients during initial processing.

Pressure

There were no casts where the CTD pressure was logging in air. No adjustments were made to the values resulting from application of manufacturer's coefficients during the initial processing.

Beam attenuation

Coefficients M and B were calculated, allowing calibration of the transmissometer with air readings taken during the cruise. M and B are calculated according to SBE Application Note No. 7:

M = (Tw/W0)*(A0-Y0)/(A1-Y1)

B= -M*Y1

Where Tw is the percent transmission for pure water for the instrument (92.98%); W0 is the voltage output in pure water (4.649 volts); A0 is the manufacturer's air voltage (4.661 volts); Y0 is the manufacturer's blocked path voltage (0.000 volts); A1 is the cruise maximum air voltage (4.31380 volts); Y1 is the current blocked path voltage (0.00 volts). For this cruise, M and B were calculated to be 21.6097 and 0, respectively.

M and B are then inserted into the following equations (from SBE Application Note No. 7) to obtain calibrated beam attenuation:

PAR

During instrument deployment, no effort was made to avoid data collection possibly being affected by ship shadowing. The LI-COR LI-192SB sensor number 69 was calibrated from raw voltages using the CEFAS supplied equation:

The Natural Environment Research Council (NERC) funds the Oceans 2025 programme, which was originally planned in the context of NERC's 2002-2007 strategy and later realigned to NERC's subsequent strategy (Next Generation Science for Planet Earth; NERC 2007).

Who is involved in the programme?

The Oceans 2025 programme was designed by and is to be implemented through seven leading UK marine centres. The marine centres work together in coordination and are also supported by cooperation and input from government bodies, universities and other partners. The seven marine centres are:

National Oceanography Centre, Southampton (NOCS)

Plymouth Marine Laboratory (PML)

Marine Biological Association (MBA)

Sir Alister Hardy Foundation for Marine Science (SAHFOS)

Proudman Oceanographic Laboratory (POL)

Scottish Association for Marine Science (SAMS)

Sea Mammal Research Unit (SMRU)

Oceans2025 provides funding to three national marine facilities, which provide services to the wider UK marine community, in addition to the Oceans 2025 community. These facilities are:

British Oceanographic Data Centre (BODC), hosted at POL

Permanent Service for Mean Sea Level (PSMSL), hosted at POL

Culture Collection of Algae and Protozoa (CCAP), hosted at SAMS

The NERC-run Strategic Ocean Funding Initiative (SOFI) provides additional support to the programme by funding additional research projects and studentships that closely complement the Oceans 2025 programme, primarily through universities.

What is the programme about?

Oceans 2025 sets out to address some key challenges that face the UK as a result of a changing marine environment. The research funded through the programme sets out to increase understanding of the size, nature and impacts of these changes, with the aim to:

improve knowledge of how the seas behave, not just now but in the future;

help assess what that might mean for the Earth system and for society;

assist in developing sustainable solutions for the management of marine resources for future generations;

enhance the research capabilities and facilities available for UK marine science.

In order to address these aims there are nine science themes supported by the Oceans 2025 programme:

Climate, circulation and sea level (Theme 1)

Marine biogeochemical cycles (Theme 2)

Shelf and coastal processes (Theme 3)

Biodiversity and ecosystem functioning (Theme 4)

Continental margins and deep ocean (Theme 5)

Sustainable marine resources (Theme 6)

Technology development (Theme 8)

Next generation ocean prediction (Theme 9)

Integration of sustained observations in the marine environment (Theme 10)

In the original programme proposal there was a theme on health and human impacts (Theme 7). The elements of this Theme have subsequently been included in Themes 3 and 9.

When is the programme active?

The programme started in April 2007 with funding for 5 years.

Brief summary of the programme fieldwork/data

Programme fieldwork and data collection are to be achieved through:

physical, biological and chemical parameters sampling throughout the North and South Atlantic during collaborative research cruises aboard NERC's research vessels RRS Discovery, RRS James Cook and RRS James Clark Ross;

the Continuous Plankton Recorder being deployed by SAHFOS in the North Atlantic and North Pacific on 'ships of opportunity';

physical parameters measured and relayed in near real-time by fixed moorings and ARGO floats;

The data is to be fed into models for validation and future projections. Greater detail can be found in the Theme documents.

Oceans 2025 Theme 10

Oceans 2025 is a strategic marine science programme, bringing marine researchers together to increase people's knowledge of the marine environment so that they are better able to protect it for future generations.

Theme 10: Integration of Sustained Observations in the Marine Environment spans all marine domains from the sea-shore to the global ocean, providing data and knowledge on a wide range of ecosystem properties and processes (from ocean circulation to biodiversity) that are critical to understanding Earth system behaviour and identifying change. They have been developed not merely to provide long-term data sets, but to capture extreme or episodic events, and play a key role in the initialisation and validation of models. Many of these SOs will be integrated into the newly developing UK Marine Monitoring Strategy - evolving from the Defra reports Safeguarding our Seas (2002) and Charting Progress (2005), thus contributing to the underpinning knowledge for national marine stewardship. They will also contribute to the UK GOOS Strategic Plan (IACMST, 2006) and the Global Marine Assessment.

Sustained, systematic observations of the ocean and continental shelf seas at appropriate time and space scales allied to numerical models are key to understanding and prediction. In shelf seas these observations address issues as fundamental as 'what is the capacity of shelf seas to absorb change?' encompassing the impacts of climate change, biological productivity and diversity, sustainable management, pollution and public health, safety at sea and extreme events. Advancing understanding of coastal processes to use and manage these resources better is challenging; important controlling processes occur over a broad range of spatial and temporal scales which cannot be simultaneously studied solely with satellite or ship-based platforms.

Considerable effort has been spent by the Proudman Oceangraphic Laboratory (POL) in the years 2001 - 2006 in setting up an integrated observational and now-cast modelling system in Liverpool Bay (see Figure), with the recent POL review stating the observatory was seen as a leader in its field and a unique 'selling' point of the laboratory. Cost benefit analysis (IACMST, 2004) shows that benefits really start to accrue after 10 years. In 2007 - 2012 exploitation of (i) the time series being acquired, (ii) the model-data synthesis and (iii) the increasingly available quantities of real-time data (e.g. river flows) can be carried out through Sustained Observation Activity (SO) 11, to provide an integrated assessment and short term forecasts of the coastal ocean state.

Overall Aims and Purpose of SO 11

To continue and enlarge the scope of the existing coastal observatory in Liverpool Bay to routinely monitor the northern Irish Sea

To develop the synthesis of measurements and models in the coastal ocean to optimize measurement arrays and forecast products. Driving forward shelf seas' operational oceanography with the direct objective of improving the national forecasting capability, expressed through links to the National Centre for Ocean Forecasting (NCOF)

To exploit the long time-series of observations and model outputs to: a) identify the roles of climate and anthropogenic inputs on the coastal ocean's physical and biological functioning (including impacts of nutrient discharges, offshore renewable energy installations and fishing activity) taking into consideration the importance of events versus mean storms / waves, river discharge / variable salinity stratification / horizontal gradients; b) predict the impacts of climate change scenarios; and c) provide new insights to Irish Sea dynamics for variables either with seasonal cycles and interannual variability, or which show weak or no seasonal cycles

To provide and maintain a 'laboratory' within which a variety of observational and model experiments can be undertaken (Oceans 2025 Themes 3, 6, 8, 9), including capture of extreme events

Demonstrate the value of an integrated approach in assessment and forecasting

Demonstrate the coastal observatory as a tool for marine management strategies through collaboration with the Environment Agency (EA), Department for Environment, Food and Rural Affairs (DEFRA), Joint Nature Conservation Commmittee (JNCC), English Nature (EN), Department of Agriculture and Rural Development (DARD), and Local Authorities, providing management information pertinent to policy (e.g. Water Framework Directive)

Fixed Station Information

Station Name

Coastal Observatory Site 2

Category

Offshore area

Latitude

53° 37.07' N

Longitude

3° 13.50' W

Water depth below MSL

11.5 m

Liverpool Bay Coastal Observatory Site 2

This station is one of 34 stations regularly visited by the Proudman Oceanographic Laboratory (POL) as part of the Liverpool Bay Coastal Observatory. During each site visit, CTD profiles are taken. The station lies within a box of mean water depth 11.5 m with the following co-ordinates:

Box Corner

Latitude

Longitude

North-west corner

53.62401°

-3.23251°

South-east corner

53.61184°

-3.21753°

The position of this station relative to the other POL Coastal Observatory sites can be seen from the figure below.

CTD Sampling History

Year

Number of Visits

Total Casts per year

2011

5

5

2010

6

6

2009

6

6

2008

6

6

2007

8

8

2006

7

7

2005

8

8

2004

9

9

2003

10

10

2002

4

4

The CTD instrument package for these cruises was a Sea-Bird 911plus, with beam transmissometer, fluorometer, LICOR PAR sensor, LISST-25, and oxygen sensor.